Imaging flow cytometry for phytoplankton analysis

Dashkova, Veronika; Malashenkov, Dmitry; Poulton, Nicole; Vorobjev, Ivan A.; Barteneva, Natasha S.

doi:10.1016/j.ymeth.2016.05.007

Cited by 83 publications

(51 citation statements)

References 133 publications

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“…The use of in-flow systems (e.g., flow cytometry) have routinely been used to assess plankton communities, including different size fractions (Dashkova et al, 2017). Using these technologies in high frequency monitoring of plankton has demonstrated that short-term events can be easily missed with sampling frequencies typically employed for monitoring (Thyssen et al, 2008;Campbell et al, 2013;Dugenne et al, 2014).…”

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confidence: 99%

Phytoplankton Community Dynamic: A Driver for Ciliate Trophic Strategies

et al. 2018

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Phytoplankton plays a key role as primary producers and mediating biogeochemical cycles in the water column. The understanding of the temporal dynamic of primary grazers channeling energy and carbon from primary producers is important for evaluating aquatic ecosystems functioning. This study investigates the coupling between phytoplankton and ciliates from live samples collected with approximately daily frequency during an almost 2-year cycle. The study site is a nutrient-rich temperate estuary, Roskilde Fjord (Denmark). Our aim is to evaluate the importance of protist grazers, especially ciliates, as predators on phytoplankton and to evaluate differences among multiple nutritional strategies through different seasons. The phytoplankton community, was mostly dominated by small organisms (<20 µm) with few observations of diatoms. In most of observations, heterotrophic dinoflagellates biomass was smaller than biomass of ciliates (<10%), indicating that ciliates are the main component of microzooplankton. Except for the spring 2016, the ciliate community closely followed the phytoplankton community, showing a tight coupling between the primary producers and grazers during all seasons. This somehow contradicts the general assumption that ciliate dominance is restricted to periods of nutrient limitation dominated by the microbial food web and suggests a year-round key role of ciliates as consumers of phytoplankton biomass. Biomasses of ciliates increased during spring and were highest during summer. Relative importance of mixotrophs were high due to occurrence of Mesodinium rubrum blooms as well as other mixotrophic ciliates in late spring/early summer. M. rubrum biomass had the opposite pattern of the cryptophyte prey Teleaulax spp., and the coupling between the two populations was very strong in late spring. Ciliates that grazed on selected phytoplankton, had a smaller potential grazing impact regarding their biomasses, likely due to food limitation; conversely ciliates that feed on diverse prey items were less constrained by food limitation, and their seasonality appear to be driven by other factors. These findings suggest that the ciliate community structure and dynamics is important in structuring the phytoplankton community on short and seasonal scale.

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confidence: 99%

Phytoplankton Community Dynamic: A Driver for Ciliate Trophic Strategies

et al. 2018

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“…To date, several studies have examined natural phytoplankton communities using IFC, such as FlowCam (Fluid Imaging Technologies, Inc., Scarborough) (39-41), CytoSense (CytoBuoy b.v., Woerden, the Netherlands) (42,43) or FlowCytobot (McLANE Research Laboratories, Inc., East Falmouth) (44). Since 2009, the ImageStream X Mk II (Luminex, Austin, Texas) IFC has been available and used mainly for biomedical research, only occasionally has it been used for phytoplankton analysis (45,46). Nevertheless, certain technical limitations still occur.…”

Section: Imaging Flow Cytometrymentioning

confidence: 99%

“…For taxa in the size range of 2-30 μm, this magnification is not sufficient for distinguishing species due to poor resolution (45). Since 2009, the ImageStream X Mk II (Luminex, Austin, Texas) IFC has been available and used mainly for biomedical research, only occasionally has it been used for phytoplankton analysis (45,46). This instrument covers a broad cell size range using three different magnifications (20×, 40×, and 60×) for particle imaging.…”

Section: Imaging Flow Cytometrymentioning

confidence: 99%

Hidden Secrets Behind Dots: Improved Phytoplankton Taxonomic Resolution Using High‐Throughput Imaging Flow Cytometry

Dunker

2019

Cytometry Pt A

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Phytoplankton are aquatic, microscopically small primary producers, accounting for almost half of the worldwide carbon fixation. As early indicators of environmental change, they play a crucial role in water quality management. Human activities like climate change, eutrophication, or international shipping traffic strongly impact diversity of these organisms. Phytoplankton monitoring is a crucial step in the recognition of changes in community composition. The common standard for monitoring programs is manual microscopic counting, which strongly limits sample number and sampling frequency. In contrast, high-throughput technologies like standard flow cytometry (FCM) are restricted to a low taxonomic resolution, which makes them unsuitable for the identification of indicator species. Imaging flow cytometers (IFC) could overcome these limitations as they combine microscopy and high-throughput analysis. In comparison to single fluorescence values, image information not only allows for a wide variety of possibilities to characterize different species as well as immediate and fast measurements but also provides an archivable data output. Taxonomic resolution of IFC (ImageStream X Mk II) was proven comparable to standard FCM (FACSAria II) by the help of numerical evaluations. This is demonstrated on different levels of taxonomic differentiation of laboratory grown cultures in this study. Phytoplankton species discrimination by an imaging flow cytometer could be useful as supportive tool to make machine-learning classifications more robust, reliable, and flexible. Furthermore, this study provides examples, demonstrating the possibility of discrimination between species with similar fluorescence properties, strains, and even subpopulations. In contrast to standard FCM, each cell is not only represented as a dot in a cytogram but is also linked to microscopic brightfield and the author presents a new way to visualize this as image-based cytograms. The source code is supplied and could be useful for all kind of IFC data in general.

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“…A recent review by Pereira et al 21 detailed FACS principles and applications with special emphasis on microalgal strain development. A few more reviews, by Hyka et al, 69 Hildebrand et al 105 and Daskova et al, 106 have discussed various flow cytometry methods including imaging flow cytometry, in line with applied microalgal biotechnology. Flow cytometry can be potentially applied in microalgal biotechnology with a wide range of prospective applications including culture purification, novel strain isolation and strain improvement.…”

Section: Applications Of Flow Cytometry In Oleaginous Microorganismsmentioning

confidence: 99%

Role of flow cytometry for the improvement of bioprocessing of oleaginous microorganisms

Sonowal

Chikkaputtaiah

Velmurugan

2019

J of Chemical Tech & Biotech

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Oleaginous microorganisms, such as yeast, fungi, microalgae and bacteria, represent a key segment of second generation feed‐stock materials and are considered to synthesize a wide range of industrially important chemical compounds. Oleaginous microorganisms possess a broad varieties of chemical compounds such as carotenoids, pigments, carbohydrates, chlorophyll, and storage‐material lipids. Oleaginous microorganisms have been recognized as promising sources for the synthesis of unsaturated, especially polyunsaturated fatty acids (PUFA). So far, a variety of high‐throughput screening methodologies (HTMs) have been employed for the development of bioprocessing of oleaginous microorganisms for sustainable production of industrially valuable compounds. Of HTMs, flow cytometry (FC) and sorters (FACS) have received substantial interest as better HTMs because of their ability to screen large numbers of cells within seconds, and interrogate and isolate living cells at single‐cell level. Forward and side scattering signals of FC are used to determine the physiological state of the cell while different channels available in the FC facilitate the detection of signals produced from fluorophores. Simultaneous measurement of physiological characteristics along with specific compound accumulation at single‐cell level enables the possibility of separating a particular phenotype with specific properties from a population. Different microbial strain development strategies in combination with FACS produced improved phenotypes with desired properties. This review first summarizes the FACS methodologies suitable for oleaginous microorganisms and the significant progress that has been achieved in oleaginous microorganisms using FACS, and highlights the important, advanced and future prospects of FACS methodologies that are suitable for the development of bioprocessing in oleaginous microorganisms. © 2018 Society of Chemical Industry

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Imaging flow cytometry for phytoplankton analysis

Cited by 83 publications

References 133 publications

Phytoplankton Community Dynamic: A Driver for Ciliate Trophic Strategies

Phytoplankton Community Dynamic: A Driver for Ciliate Trophic Strategies

Hidden Secrets Behind Dots: Improved Phytoplankton Taxonomic Resolution Using High‐Throughput Imaging Flow Cytometry

Role of flow cytometry for the improvement of bioprocessing of oleaginous microorganisms

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